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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ) $local_species = 'din' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ), 'gf_id' => 'HOM05D001330', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001330' ), 'data_identifier' => 'HOM05D001330', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001330', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '472', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p13910' => 'bna', 'A02p13920' => 'bna', 'A02p13950' => 'bna', 'A04p11330' => 'bna', 'A04p11340' => 'bna', 'A04p11400' => 'bna', 'A04p15370' => 'bna', 'A07p19690' => 'bna', 'Aa31LG2G3490' => 'aar', 'Aa31LG9G17090' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.3163' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.261' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2064' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.2836' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.4068' => 'aag', 'Actinidia14891' => 'ach', 'Actinidia16653' => 'ach', 'Actinidia17315' => 'ach', 'Actinidia38630' => 'ach', 'Ah.01g008270' => 'amhyb', 'Ah.01g023080' => 'amhyb', 'Ah.10g037800' => 'amhyb', 'Ah.10g037830' => 'amhyb', 'Ah.10g037840' => 'amhyb', 'Ah.16g101810' => 'amhyb', 'AL2G25460' => 'aly', 'AL7G52150' => 'aly', 'AL7G52160' => 'aly', 'AL7G52170' => 'aly', 'Aqoxy3G00296' => 'aox', 'Aqoxy3G00297' => 'aox', 'Aqoxy7G03027' => 'aox', 'arahy.Tifrunner.gnm1.ann1.97RMNS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FHUH7B' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HCT4KE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I56F9F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K6N5RU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XT6T0B' => 'arhy', 'AT1G67090' => 'ath', 'AT5G38410' => 'ath', 'AT5G38420' => 'ath', 'AT5G38430' => 'ath', 'ATR0709G044' => 'atr', 'ATR1125G107' => 'atr', 'Atru.chr1.1703' => 'acertr', 'Atru.chr11.73' => 'acertr', 'Atru.chr11.74' => 'acertr', 'Atru.chr11.75' => 'acertr', 'Atru.chr7.595' => 'acertr', 'AUR62008991' => 'cqu', 'AUR62008993' => 'cqu', 'AUR62008994' => 'cqu', 'AUR62018154' => 'cqu', 'AUR62023307' => 'cqu', 'AUR62023308' => 'cqu', 'AUR62023310' => 'cqu', 'AUR62035539' => 'cqu', 'AUR62042566' => 'cqu', 'BcaB02g08009' => 'bca', 'BcaB05g24235' => 'bca', 'BcaB06g27199' => 'bca', 'BcaB06g27202' => 'bca', 'BcaB06g27219' => 'bca', 'BcaB06g27713' => 'bca', 'BcaB06g27715' => 'bca', 'BcaC02g08874' => 'bca', 'BcaC02g09646' => 'bca', 'BcaC03g14794' => 'bca', 'BcaC03g14795' => 'bca', 'BcaC03g14798' => 'bca', 'BcaC08g44378' => 'bca', 'BolC2t08396H' => 'bol', 'BolC2t08397H' => 'bol', 'BolC2t08399H' => 'bol', 'BolC4t26081H' => 'bol', 'BolC4t26082H' => 'bol', 'BolC4t26088H' => 'bol', 'BolC4t26547H' => 'bol', 'BolC6t37020H' => 'bol', 'BraA02t06452Z' => 'bra', 'BraA02t06453Z' => 'bra', 'BraA04t16794Z' => 'bra', 'BraA04t16795Z' => 'bra', 'BraA04t16802Z' => 'bra', 'BraA04t17177Z' => 'bra', 'BraA07t29669Z' => 'bra', 'C02p22410' => 'bna', 'C02p22420' => 'bna', 'C02p22460' => 'bna', 'C04p45030' => 'bna', 'C04p45040' => 'bna', 'C04p45090' => 'bna', 'C04p49600' => 'bna', 'C06p18120' => 'bna', 'CAN.G225.2' => 'can', 'CAN.G625.14' => 'can', 'CAN.G625.17' => 'can', 'CAN.G625.18' => 'can', 'CAN.G625.20' => 'can', 'CAN.G625.21' => 'can', 'CAN.G625.22' => 'can', 'CAN.G82.8' => 'can', 'CANSAT01G1858' => 'cansat', 'CANSAT11G1652' => 'cansat', 'CANSAT11G1916' => 'cansat', 'CANSAT21G2461' => 'cansat', 'CANSAT78G2503' => 'cansat', 'CARHR059540' => 'chi', 'CARHR214170' => 'chi', 'Carub.0002s1338' => 'cru', 'Carub.0007s3758' => 'cru', 'Carub.0007s3759' => 'cru', 'Carub.0007s3760' => 'cru', 'Ca_04054_v3' => 'car', 'Ca_04055_v3' => 'car', 'CBR_g19695' => 'cbr', 'CBR_g19696' => 'cbr', 'CBR_g37370' => 'cbr', 'CBR_g46359' => 'cbr', 'Cc00_g15710' => 'ccan', 'Cc00_g28090' => 'ccan', 'Cc06_g13150' => 'ccan', 'CDE04G3186' => 'cde', 'CDE06G1089' => 'cde', 'CDE06G2399' => 'cde', 'CDE07G0305' => 'cde', 'Cfa007927' => 'cfa', 'Cfa013496' => 'cfa', 'Cfa018593' => 'cfa', 'Ciclev10009532m.g' => 'ccl', 'Ciclev10012893m.g' => 'ccl', 'Ciclev10023403m.g' => 'ccl', 'CiPaw.03G061200' => 'cil', 'CiPaw.07G193000' => 'cil', 'CiPaw.15G085400' => 'cil', 'CiPaw.15G085500' => 'cil', 'ClCG05G022680' => 'cla', 'COL.COLO4_09321' => 'col', 'COL.COLO4_09322' => 'col', 'COL.COLO4_09323' => 'col', 'COL.COLO4_37735' => 'col', 'COL.COLO4_37758' => 'col', 'Cpa.g.sc1.37' => 'cpa', 'Cpa.g.sc1.38' => 'cpa', 'Cpa.g.sc1021.2' => 'cpa', 'Cpa.g.sc282.14' => 'cpa', 'Cre02.g120100' => 'cre', 'Cre02.g120150' => 'cre', 'CsaV3_5G034360' => 'csa', 'CSS0015687' => 'camsi', 'CSS0024931' => 'camsi', 'CSS0028701' => 'camsi', 'CSS0042222' => 'camsi', 'Dinv15671' => 'din', 'Dinv28103' => 'din', 'Dinv31637' => 'din', 'Dinv34825' => 'din', 'Dinv41232' => 'din', 'Dinv42712' => 'din', 'Dinv43389' => 'din', 'Duzib133G0331' => 'dzi', 'Duzib168G0629' => 'dzi', 'ECA232G3191' => 'eca', 'ECA234G0910' => 'eca', 'EL10Ac2g04573' => 'bvu', 'EL10Ac2g04574' => 'bvu', 'EL10Ac2g04576' => 'bvu', 'EL10As19g24198' => 'bvu', 'Eucgr.B03013' => 'egr', 'Eucgr.C00150' => 'egr', 'Eucgr.J01502' => 'egr', 'Eucgr.K02223' => 'egr', 'FAN02G2187' => 'fan', 'FAN05G2828' => 'fan', 'FAN07G0364' => 'fan', 'FAN07G1973' => 'fan', 'FAN09G4444' => 'fan', 'FAN12G0957' => 'fan', 'FAN12G2384' => 'fan', 'FAN12G2562' => 'fan', 'FAN17G0873' => 'fan', 'FAN22G1028' => 'fan', 'FvH4_4g08000' => 'fve', 'FvH4_4g27330' => 'fve', 'FvH4_6g26030' => 'fve', 'Glyma.13G046200' => 'gma', 'Glyma.13G097100' => 'gma', 'Glyma.14G089500' => 'gma', 'Glyma.18G296900' => 'gma', 'Glyma.19G046600' => 'gma', 'Glyma.19G046800' => 'gma', 'Glyma.19G047000' => 'gma', 'Gohir.A03G022400' => 'ghi', 'Gohir.A07G173466' => 'ghi', 'Gohir.A11G163200' => 'ghi', 'Gohir.A11G163300' => 'ghi', 'Gohir.D03G146300' => 'ghi', 'Gohir.D07G180900' => 'ghi', 'Gohir.D11G169600' => 'ghi', 'Gohir.D11G169700' => 'ghi', 'Gorai.001G201800' => 'gra', 'Gorai.003G153700' => 'gra', 'Gorai.007G181300' => 'gra', 'Gorai.007G181400' => 'gra', 'GSVIVG01008288001' => 'vvi', 'GSVIVG01029221001' => 'vvi', 'HanXRQChr10g0308491' => 'han', 'HanXRQChr11g0325011' => 'han', 'HanXRQChr11g0325331' => 'han', 'HanXRQChr11g0325341' => 'han', 'HanXRQChr11g0325351' => 'han', 'HanXRQChr11g0325361' => 'han', 'HanXRQChr11g0330621' => 'han', 'HanXRQChr12g0365931' => 'han', 'HanXRQChr16g0523951' => 'han', 'HanXRQChr16g0524811' => 'han', 'HanXRQChr17g0563041' => 'han', 'Haze_14148' => 'cav', 'Haze_17486' => 'cav', 'Haze_22085' => 'cav', 'Hma1.2p1_1109F.1_g257960' => 'hma', 'HPP92_020144' => 'vpl', 'Hund13721' => 'sun', 'Hund16152' => 'sun', 'Lalb_Chr04g0257441' => 'lal', 'Lalb_Chr06g0174591' => 'lal', 'Lalb_Chr10g0091251' => 'lal', 'Lalb_Chr10g0100001' => 'lal', 'Lalb_Chr13g0300171' => 'lal', 'Lalb_Chr21g0317841' => 'lal', 'Lj1g0001864' => 'lja', 'Lj1g0008098' => 'lja', 'Lj1g0019339' => 'lja', 'Lj2g0016211' => 'lja', 'Lj4A191T52' => 'lonja', 'Lj4g0027235' => 'lja', 'Lj6A758T17' => 'lonja', 'Lj6A758T18' => 'lonja', 'Lju583A4T33' => 'lonja', 'Lsat_1_v5_gn_2_79481' => 'lsa', 'Lsat_1_v5_gn_2_79501' => 'lsa', 'Lsat_1_v5_gn_2_79541' => 'lsa', 'Lsat_1_v5_gn_2_79581' => 'lsa', 'Lsat_1_v5_gn_2_79600' => 'lsa', 'Lsat_1_v5_gn_4_153980' => 'lsa', 'Lsat_1_v5_gn_4_31161' => 'lsa', 'Lsat_1_v5_gn_5_85080' => 'lsa', 'Manes.01G011500' => 'mes', 'Manes.05G137400' => 'mes', 'Manes.06G023400' => 'mes', 'Mapoly0011s0069' => 'mpo', 'Mapoly0011s0071' => 'mpo', 'Mapoly0070s0039' => 'mpo', 'Mapoly0114s0049' => 'mpo', 'Mapoly0114s0050' => 'mpo', 'Mapoly0114s0051' => 'mpo', 'Mapoly0114s0052' => 'mpo', 'Mapoly0114s0053' => 'mpo', 'Mapoly0114s0054' => 'mpo', 'Mapoly0114s0055' => 'mpo', 'Mapoly0114s0056' => 'mpo', 'Mapoly0114s0057' => 'mpo', 'Mapoly0119s0030' => 'mpo', 'Mapoly0119s0031' => 'mpo', 'Mapoly0132s0032' => 'mpo', 'Mapoly0146s0013' => 'mpo', 'Mapoly0146s0014' => 'mpo', 'Mapoly0146s0015' => 'mpo', 'Mapoly2802s0001' => 'mpo', 'Mapoly2802s0002' => 'mpo', 'MBI16_g31782_MAGBIO' => 'mbi', 'MBI16_g35166_MAGBIO' => 'mbi', 'MCO09G375' => 'mco', 'MCO09G573' => 'mco', 'MD04G1188500' => 'mdo', 'MD09G1252100' => 'mdo', 'MD13G1041800' => 'mdo', 'MD13G1041900' => 'mdo', 'MD13G1252300' => 'mdo', 'MD16G1042700' => 'mdo', 'MD17G1244400' => 'mdo', 'Medtr4g127870' => 'mtr', 'Medtr6g018300' => 'mtr', 'Medtr6g018310' => 'mtr', 'Medtr7g007120' => 'mtr', 'Medtr7g007200' => 'mtr', 'Medtr7g007210' => 'mtr', 'Medtr7g007220' => 'mtr', 'Medtr7g007230' => 'mtr', 'MELO3C012252.2' => 'cme', 'Migut.D01471' => 'egut', 'Migut.D01473' => 'egut', 'Migut.H00214' => 'egut', 'Migut.I00348' => 'egut', 'Migut.J01492' => 'egut', 'MSTRG.4508' => 'ama', 'MSTRG.9569' => 'ama', 'Nitab4.5_0000055g0290' => 'nta', 'Nitab4.5_0000055g0300' => 'nta', 'Nitab4.5_0000659g0110' => 'nta', 'Nitab4.5_0000659g0120' => 'nta', 'Nitab4.5_0000659g0130' => 'nta', 'Nitab4.5_0000682g0090' => 'nta', 'Nitab4.5_0000912g0250' => 'nta', 'Nitab4.5_0000912g0260' => 'nta', 'Nitab4.5_0000912g0270' => 'nta', 'Nitab4.5_0000912g0280' => 'nta', 'Nitab4.5_0001382g0020' => 'nta', 'Nitab4.5_0002207g0050' => 'nta', 'Nitab4.5_0006249g0010' => 'nta', 'Nitab4.5_0020038g0010' => 'nta', 'Nn1g05779' => 'nnu', 'Nn3g17846' => 'nnu', 'Nn4g23841' => 'nnu', 'Nn4g23842' => 'nnu', 'Nn4g23843' => 'nnu', 'Oeu031819.1' => 'oeu', 'Oeu058030.1' => 'oeu', 'Os02g0152400' => 'osa', 'Os12g0274700' => 'osa', 'Os12g0291200' => 'osa', 'Os12g0291400' => 'osa', 'Os12g0292400' => 'osa', 'Peaxi162Scf00104g00083' => 'pax', 'Peaxi162Scf00231g01221' => 'pax', 'Peaxi162Scf00394g00425' => 'pax', 'Peaxi162Scf00394g00510' => 'pax', 'Peaxi162Scf00501g00021' => 'pax', 'PGR042G0189' => 'pgr', 'PGR044G1281' => 'pgr', 'PGSC0003DMG400004097' => 'stu', 'PGSC0003DMG400012666' => 'stu', 'PGSC0003DMG400019584' => 'stu', 'PGSC0003DMG400024182' => 'stu', 'PGSC0003DMG400026409' => 'stu', 'Phvul.004G064800' => 'pvu', 'Phvul.004G073400' => 'pvu', 'Phvul.004G073450' => 'pvu', 'Potri.004G100000' => 'ptr', 'Potri.006G167901' => 'ptr', 'Potri.017G114600' => 'ptr', 'Potri.018G091401' => 'ptr', 'Pp3c10_3140' => 'ppa', 'Pp3c12_11880' => 'ppa', 'Pp3c12_12340' => 'ppa', 'Pp3c12_19890' => 'ppa', 'Pp3c12_7010' => 'ppa', 'Pp3c12_7030' => 'ppa', 'Pp3c13_15786' => 'ppa', 'Pp3c13_15800' => 'ppa', 'Pp3c13_15910' => 'ppa', 'Pp3c13_15980' => 'ppa', 'Pp3c13_16000' => 'ppa', 'Pp3c13_16130' => 'ppa', 'Pp3c15_22720' => 'ppa', 'Pp3c15_22730' => 'ppa', 'Pp3c16_12810' => 'ppa', 'Pp3c19_1840' => 'ppa', 'Pp3c19_1860' => 'ppa', 'Pp3c19_3190' => 'ppa', 'Pp3c19_7460' => 'ppa', 'Pp3c22_540' => 'ppa', 'Pp3c22_7400' => 'ppa', 'Pp3c2_4100' => 'ppa', 'Pp3c3_12330' => 'ppa', 'Pp3c3_12530' => 'ppa', 'Pp3c3_14480' => 'ppa', 'Pp3c3_14510' => 'ppa', 'Pp3c3_18750' => 'ppa', 'Pp3c3_20110' => 'ppa', 'Pp3c3_20140' => 'ppa', 'Pp3c4_11770' => 'ppa', 'Pp3c4_13260' => 'ppa', 'Pp3c4_4820' => 'ppa', 'PRCOL_00001220' => 'pco', 'PRCOL_00001221' => 'pco', 'PRCOL_00004521' => 'pco', 'PRCOL_00004522' => 'pco', 'Prupe.1G084500' => 'ppe', 'Prupe.1G311400' => 'ppe', 'Prupe.3G157200' => 'ppe', 'Prupe.4G198400' => 'ppe', 'Psat1g080440' => 'psa', 'Psat3g204960' => 'psa', 'Psat3g205000' => 'psa', 'Psat3g205160' => 'psa', 'Psat3g205200' => 'psa', 'Psat3g205240' => 'psa', 'Psat3g205280' => 'psa', 'Psat4g012920' => 'psa', 'PSO063G7130' => 'pso', 'PSO170G1335' => 'pso', 'PSO170G1589' => 'pso', 'PSO170G3867' => 'pso', 'PSO478G1453' => 'pso', 'PSO675G2408' => 'pso', 'PSO675G5533' => 'pso', 'PSO675G7529' => 'pso', 'PSO732G0222' => 'pso', 'PSO732G0289' => 'pso', 'PSO732G0736' => 'pso', 'PSO782G0902' => 'pso', 'PSO782G1067' => 'pso', 'PSO782G1741' => 'pso', 'QL02p052407' => 'qlo', 'QL02p097931' => 'qlo', 'RcHm_v2.0_Chr2g0126111' => 'rch', 'RcHm_v2.0_Chr4g0401741' => 'rch', 'RcHm_v2.0_Chr4g0435151' => 'rch', 'Rhsim10G0066900' => 'rsi', 'Rhsim12G0085000' => 'rsi', 'Sabra04G0079900' => 'sbr', 'Sabra17G0094900' => 'sbr', 'SalBow5G0027' => 'sbo', 'SalBow5G3230' => 'sbo', 'SalBow5G5241' => 'sbo', 'Sc10g0001200' => 'sci', 'Sc11g0008310' => 'sci', 'Sc11g0008320' => 'sci', 'Sed0014916' => 'sed', 'SEGI_12641' => 'sgi', 'SEGI_20021' => 'sgi', 'SEGI_39244' => 'sgi', 'SGA_v2.0_scaffold42G16027' => 'sas', 'SGA_v2.0_scaffold66G22416' => 'sas', 'SMO111G0174' => 'smo', 'SMO232G0094' => 'smo', 'Solyc02g063150.3' => 'sly', 'Solyc02g085940.4' => 'sly', 'Solyc02g085950.4' => 'sly', 'Solyc03g034220.3' => 'sly', 'Solyc07g017950.3' => 'sly', 'Sopen02g014220' => 'spe', 'Sopen02g030610' => 'spe', 'Sopen02g030630' => 'spe', 'Sopen03g007000' => 'spe', 'Sopen07g006810' => 'spe', 'Sp5g22020' => 'spa', 'TAR371G0931' => 'tar', 'TAR374G0087' => 'tar', 'TAR622G0141' => 'tar', 'TAR622G0312' => 'tar', 'TAR627G0034' => 'tar', 'TAR636G1852' => 'tar', 'THA.LOC104800009' => 'tha', 'THA.LOC104803942' => 'tha', 'THA.LOC104821932' => 'tha', 'Thecc.02G230300' => 'tca', 'Thecc.02G230600' => 'tca', 'Thecc.03G035100' => 'tca', 'Thecc.04G134500' => 'tca', 'Thecc.09G176100' => 'tca', 'Thhalv10019199m.g' => 'esa', 'Thhalv10019202m.g' => 'esa', 'Thhalv10027955m.g' => 'esa', 'TPR.G32462' => 'tpr', 'TPR.G40756' => 'tpr', 'TPR.G40847' => 'tpr', 'TWI32G1034' => 'twi', 'TWI53G1994' => 'twi', 'TWI77G0921' => 'twi', 'unitig_32.g10655' => 'ugi', 'unitig_32.g11890' => 'ugi', 'unitig_748.g8753' => 'ugi', 'unitig_88.g27806' => 'ugi', 'vmacro01386' => 'vma', 'vmacro05559' => 'vma', 'vmacro06009' => 'vma', 'VMungo0464G0555' => 'vmu', 'VMungo1215G1836' => 'vmu', 'Zm00001eb092540' => 'zma', 'Zm00001eb197410' => 'zma' ) $gf_id = 'HOM05D001330' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001330' ) $data_identifier = 'HOM05D001330' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 16, 'aar' => (int) 2, 'aag' => (int) 5, 'ach' => (int) 4, 'amhyb' => (int) 6, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 5, 'cqu' => (int) 9, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 8, 'cansat' => (int) 5, 'chi' => (int) 2, 'cru' => (int) 4, 'car' => (int) 2, 'cbr' => (int) 4, 'ccan' => (int) 3, 'cde' => (int) 4, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 4, 'cla' => (int) 1, 'col' => (int) 5, 'cpa' => (int) 4, 'cre' => (int) 2, 'csa' => (int) 1, 'camsi' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 4, 'egr' => (int) 4, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 2, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 1, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 6, 'lja' => (int) 5, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 3, 'mpo' => (int) 20, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 7, 'mtr' => (int) 8, 'cme' => (int) 1, 'egut' => (int) 5, 'ama' => (int) 2, 'nta' => (int) 14, 'nnu' => (int) 5, 'oeu' => (int) 2, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 2, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 32, 'pco' => (int) 4, 'ppe' => (int) 4, 'psa' => (int) 8, 'pso' => (int) 14, 'qlo' => (int) 2, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 2, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 5, 'spa' => (int) 1, 'tar' => (int) 6, 'tha' => (int) 3, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 2, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb197410' $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